Tides of Darkness Revised
by Lord Vukodlak
Summary: Another tale in a dark future, Many people you knew are now dead. Giovanni rules all of Kanto. Many are trying to stop Team Rocket. Some of them may be worse then the problem
1. Welcome to Kanto

Prologue

Dark times have fallen on Kanto. It started five years after Ash started his pokemon Journey well technically it started long before he was born but it only came to light shortly after his fifteenth birth day. Vermillion city was attacked by a then unknown army genetically engineered pokemon. Lt. Surge the city's gym leader led a successful defense and saved the city. However, it cost him his life. Lance leader of the elite four started an investigation. A mysterious man who claimed he knew not only who was responsible but also, where the guilty party could be found soon approached him and the rest of the elite four.

Three days later the bodies of Lance, Agatha, Bruno and Lorelei we're all found on route 2 south of Viridian City. Team Rocket claimed responsibility for the murder. Giovanni declared himself ruler of Kanto he unleashed him army of genetically altered pokemon and rocket agents upon the peoples of Kanto. Koga gym leader of Fuchia city tried to infiltrate Team Rocket head quarters and assassinate the self appointed Emperor of Kanto. He was never seen again.

When Team Rocket attacked Celadon city Erica managed to lead many of her students to safety. However, she was captured and Giovanni hand her publicly executed in an attempt to frighten the populace into submission. Misty and her sisters were separated when team rocket set fire to the Cerulean gym. Misty and her Sister Lilly survived. I do not know about the other two. Sabrina with her immense psionic powers easily escaped captures and went underground and started one of the major resistant moments called "The High Guard"

Brock was very fortunate in that he got his entire family to safety before Team Rocket attacked Pewter. He join up with Ash and Gary who had started another major resistance group called "The Son's Of Pallet Town"

I suppose you would like to know what became of the fire gym leader Blaine. Well he did not live to see the dark times. He died laughing. Seriously he chocked to death on his chicken dinner its not funny. I'm sure Blaine would have found it historical.

It took Giovanni little more then a year to conquer Indigo. It took him almost four more years to conquer Johto. Mainly due to the fact, Johto had time to prepare. The eight gym leaders raised an army in defense of Johto planning to finish Giovanni off. It was then Giovanni unleash a new kind of pokemon. It called a "Menace", a genetically engineered pokemon. It was of both psychic and fighting type. On it has large syther like blades on each arm.

Despite there efforts one by one the gym leaders of Johto fell. Only Clair escaped no one knows where.

In just five years from Lance's death Giovanni had become the ruler of Kanto. His army gathered in ships and set sail for the Hoen Region. However, his navy was defeat by a single pokemon. Mewtwo using his powers he created a massive storm and annihilated Giovanni fleet. The storm remained, blocking Giovanni's army from spreading. Mewtwo did not have the power to stop Giovanni with out killing tens of thousands of innocent people but he could stop him from spreading his empire any further.

Five years have past sense Giovanni conquered Kanto. Alternatively, 15 years sense Ash started his journey if you haven't been keeping track. The rebellion has fault a war of harassment over the years, slowly undermining Giovanni's rule. Giovanni believes he will eventually crush the High Guard and the Son's of Pallet Town. He maybe right however he should beware.

A new power has been growing in the darkness of Kanto. "The Black Sword" is its name, years ago when Giovanni's mother Madam Boss was the leader of Team Rocket. The Black Sword led by Drake one of the most sinister men ever to live tried to destroy team rocket. He was defeated and his organization destroyed. However, I have resurrected the order of the Black Sword. My name is Kain, I am the Lord of Darkness, and I have vowed to wipe Team Rocket from the face of the earth. Let the rest of the world burn all I want is my revenge and nothing will stop me from attaining it. Giovanni had best prepare for the Tides of Darkness.


	2. Cheers

The dimly lit bar in Cerulean City was one of those basement bars kind of like Cheers but combined with a biker bar. It was the cliché reached hive of scum and villainy and a hang out for the Team Rocket agents in the city. Few people who were not associated with the Rockets would dare enter.

The bar tender was a large gruff individual. He had the eye batch and spit in the glass he wiped. He wore a torn leather jacket with the sleeves cut off. The various agents scattered about the bar sipped their drinks and complained about the rebellion in the city. The name "Vapor Vengeance" was mentioned several times.

It was then a tall blue-eyed carrot top entered the establishment. She removed her green body length jacket and hung it on the wall,

She wore tight blue pants and an even tighter red top. Her hair tied in a ponytail that went down just past the base of her neck. She caught the attention of the men in the room who stared at her swinging butt as she strolled up to the bar.

A few of the women agents slapped some of the men for being well being men.

She whispered a few things to the bar tender. The gruff man then pulled out some cash and put it on the table. The woman picked it up slipped it into her pockets. She set down her tattered black leather purse on the bar stool and walked up to the stage and microphone. She put a tape into the machine by the stage and picked up the microphone before singing.

_Out here in the quiet of the night_

_Beneath the stars and moon_

_We both know we got something on our minds_

_We wont admit, but it's true_

_You look at me I look away_

As she sung, she noticed a figure in the corner of the bar. He was a tall man 6ft 6 easily. His face concealed in the darkness of the room except for his eyes, which stared right back. The woman just went on singing.

_I want to tell you what I'm feeling _

_But I don't know how to start_

_I want to tell you but no I'm afraid that you might break my heart_

_For why should anything so easy ever be so hard to do?_

_I want to tell you what I'm feeling and just say that I love you_

_I practice all the things that I could say_

_Line by line every word_

_I tell myself that today could be the day_

_But every time I lose my nerve_

_I look at you, you look away_

A strange peace settled over the bar. She had everyone's attention. The woman could not help but look at the dark cloaked figure in the corner. His cold dark blue eyes pierced right into her soul. The man had the eyes of a killer she thought. She was more afraid of what that one man then every single Team Rocket member in the bar. She kept singing.

_I want to tell you what I'm feeling _

_But I don't know how to start_

_I want to tell you but no I'm afraid that you might break my heart_

_For why should anything so easy ever be so hard to do?_

_I want to tell you what I'm feeling and just say that I love you_

_Why, why do you turn away? _

_It must be you're afraid like me_

_I try but I cant pretend that I _

_Don't feel for you _

_The way I do_

_Can't you see?_

Toward the end of the song, she looked back and found the strange man has gone. She was relieved the man made her so nervous as if he was staring into her soul.

_I want to tell you what I'm feeling _

_But I don't know how to start_

_I want to tell you but no I'm afraid that you might break my heart_

_For why should anything so easy ever be so hard to do?_

_I want to tell you what I'm feeling and just say that I love you_

The men in the bar cheered and gave some hoots. The woman just smiled and gave a bow before heading towards the door. She put her jacket back on and left leaving the cold silence to fill the room again.

One of the agents a man with short brown hair in the standard black rocket uniform

"Hey the chick left her purse"

He walked over to the purse and picked it up.

"Dam this thing is crappy," he said.

It was then he noticed the bar tender was missing.

"What the hell where did that fat fool go!?"

The under lying truth hit the agents who dove away from the bar dropping the purse. The purse hissed before releasing smoke and sparks.

One of the agents laughed.

"Ha it was a dud!"

"And she left her tape in the machine too"

Outside the woman smiled as the bar exploded. It was snowing in the city and no one was on the street that time of night. She walked away with a laugh. She knew she permanently took out at lest four of the 12 agents in the bar. In the ensuing chaos outside the burning bar she disappeared into the night. It was snowing hard and only half the street lamps remained lit.

She walked for more then an hour down the back alleys and side streets. Normally she would be afraid of a patrol picking her up but she couldn't get the image of that dark figure in the bar. Finally, she came to run down brick warehouse. A scream in the distance startled her but she paid no mind. Even before the occupation, screams could still be heard at night. She walked around to the back past the broken barbed wire fence.

The door was rusty and battered steel. She knocked on the door and shivered in the cold of the snowy night. She heard some movement from behind the door. A slot opened up and a pair of eyes looked out at her.

"What do you want?" a gruff voice asked.

She smiled and replied. "Rebecca was the one who burned down Cheers"

The sound of locks beings undone could be heard before the door opened.

The green haired man stood aside and said with a smile.

"Welcome back to the Vapor hang out"

She stepped inside, the warehouse had only a few crates scattered about is massive interior. It was well lit the lights maintained. She was expecting to she the various rebels hanging around the old warehouse. She found six uniformed Team Rocket agents.

"Nooooo!" she screamed. She tried to rush the door but the plain clothed man grabbed her.

One of the smirking agents stood up. He was only 5ft 4 but had huge muscles. His head shaved bald and shiny. His uniform was a bit nicer then the rest the boots and gloves were shiny and polished.

"Well well boys looks like we hit it big tonight. We got every last one of those Vapor's and the leader"

The agents forced the woman to her knees. The bald rocked circled her with an evil smirk.

"What should we do with you?" he asked grabbing her chin and forcing her to look up at him.

The woman kept her eyes to the floor best she could tears streamed down her face.

"You killed them didn't you" she spat venomously.

The agents all laughed.

The bald man smiled and said.

"Yes they are. Put up quite a fight they would not reveal your location so we figured if we just had to wait for you to come back. Bruce over there looked kind of like one of the rebels so we had him answer the door" The man pulled a knife from his pocket a bowie knife to be exact, with a serrated edge.

The woman's eyes grew wide with fear.

"Now I have three options, One could kill you right here and now, two I could have you sent to viridian where you will be tortured for information, likely by use electric shock before your executed"

He gently put the point of the blade at her shirt. Fear filled the woman's eyes she knew option three.

"Three I could let the boys have some fun with you before any of the other two options"

The men all laughed and cheered for option three.

"Hey boss what about using those three Houndoons on her?" one agent said pointing to the three black dogs sitting on one of the few crates.

Before the bald man could respond, he felt a painful jab in his back and the feeling of being lifted into the air. He had been stabbed in the back with a sword.

Standing behind him holding the sword was the same dark figure from the bar. The dark figure with the piercing blue eyes tossed the bald rocket across the room.

The two agents holding the woman dropped her, she hit the ground with a thud. They reached for thier pokeballs but the Houndooms attacked them growling and biting. The third Houndoom attacked the rocket by the door.

Only two agents remained the looked at each other before trying to run for the door past the woman on the ground. The dark figure cut down the first escaping rocket. The second managed to escape and ran down the street.

The dark figure turned to the Houndooms and said "kill him," the three dogs charged off and with in seconds screams and howls could be heard in the distance.

"Your name is Misty right"

The woman, Misty stood up to face her savior. "Your him aren't you, your Kain leader of the terrorist group the Black Sword?"

The dark figure Kain grunted. "Says the woman who just blew up a bar"

Misty tightened her fists

"Your method is one of terror Kain, your name strikes fear into Team Rocket agents, you butcher them and not only do you butcher them you enjoy it to, any way thanks for the rescue I'll be going now" She turned to leave.

Kain walked up behind Misty his arm came around her and he placed a cloth to her face. She let out a muffled scream before she went unconscious.

Kain picked her up and swung her over his shoulder.

The three houndooms returned from their kill and waited for their masters orders.

Kain pulled out a phone and but it to his ear.

"Shadow I got her I'll be back before dawn" With that he walked out the door with his hounds in toe. Leaving the carnage of the slaughter behind him.


	3. Mind over Dark

Sabrina commander of the High Guard waited at the foot of mount moon. She wore the same clothing she did years ago as gym leader. Her long green hair waved in the wind. The setting sun made the clear winter sky glow that reflected off the snow a pretty sight especially in such trying times. The forest around her was quite as all the pokemon went to sleep before the pokemon of the night awoke. Only a light layer of snow littered the area.

She had no fear of patrols from Team Rocket she could handle them.

"Where is that bastard he's late!" she fumed.

"Speak of the devil and the devil shall appear" a sinister voice said. Sabrina whirled around to face him. It was Kain dressed as always in black. His hair was to short to blow in the wind but his cape blew just fine. He had his arms crossed over his chest and a smirk on his face.

Sabrina stood only 5ft 6, therefore Kain stood ten inches taller.

"Kain tell me what you've done with Misty!" She demanded. I have to be firm Sabrina thought she knew that if Kain sense any fear from her he would use it to his advantage.

Kain only shrugged and said.

"I don't know what your talking about I haven't done anything with her"

The psychic woman stood straight and looked up into Kain's eyes.

"I know you have her Kain after one of my High Guard intelligent officers reported that Team Rocket had captured the members of the group the Vapor Vengeance, and had laid a trap for its leader Misty" she said as she repeatedly poked Kain's chest.

Kain was quite annoyed with this behavior but only stared right back at her.

"Those rocket agents were found with wounds consistent with a sword and Houndoom bites, so stop trying to deny it and tell me what your doing with her and hand her over or else!" Suddenly Sabrina realized she had pushed it to far. In a flash, his hand was at her throat.

His grip was so tight she couldn't breathe. She tried to summon up her mental powers but Kain was pressing his thumb right into a pressure point the pain and lack of air made it hard to concentrate and if he pressed any harder he might kill her. Even if she could if the stories about Kain turn out to be true a physic attacks would be useless.

Instinctively Sabrina grabbed his arm and tried to pry him off.

"I admit yes she is in my custody but keep in mind if not for me she'd be dead, once I've learned what I want from the girl I'll let her go" with that he dropped Sabrina to the ground.

Kain turned away and started walking way towards the setting sun as if he never even stopped to talk to her.

Sabrina stood up and charged her power.

"Time to test the stories" the air rippled from he Kain and in and instant the ground ruptured in a line from her to Kain.

Kain was consumed in a cloud of dust.

"Did I get him?" Sabrina wondered. When the dust settled Kain was gone.

Sabrina sighed,

"Your right behind me aren't you."

"Yes" Kain smirked

Sabrina turned around to face him.

"Why the hell do you do that!"?

"You mean the appearing mysteriously behind people?" Kain laughed.

"Yes!"

"Its fun you should try it some time" Kain smirked.

Sabrina just stared into his eyes, it was good thing her attack was ineffective, otherwise she'd have to fight him.

"Maybe I can probe his mind and find out his intentions' Sabrina thought.

Sabrina closed her eyes and tried to dive right into his mind.

"Its working" she thought.

So she dove in and entered his mind, Kain only smiled he knew exactly what Sabrina was up to.

The woman winced in pain as she dove into his mind.

"What ever is the matter don't like what you see?"

Finally, Sabrina was forced to break contact. She fell to the ground unable to stand. Kain left her gasping for breath.

"So much pain" Sabrina muttered, however she was not referring to her own pain.

(Elsewhere)

Misty groaned as she came back from unconsciousness.

"Where am I?" she thought aloud. She looked around and found herself in a small stone cell. The only bars in the cell made up the door

The lights in the ceiling kept the small room well lit and the toilet thankfully was hidden from view behind a heavy curtain.

Misty went up to the door and tried to look around. She noticed she was in some kind of prison.

"Did team rocket capture me?" she thought aloud.

"LET ME OUT OF HERE!" she screamed at the top of her lungs.

She heard footsteps coming towards the cell.

"Don't worry Misty your not in the clutches of team rocket" a soft voice said.

"Who are you show your self?" Misty asked fearfully.

The man stepped into view he was dressed in black cloth like some kind of Ninja. Misty could only see his green eyes.

"My name is Shadow, don't worry Misty Kain will release in a few days"

"Where am I?" she asked.

"The obvious answer would be in a jail cell, I suppose your not in a joking mood. Your in the lair of the Black Sword"

"What do you want from me?" Misty demanded

Shadow only shrugged. "I don't really know you'd have to ask master Kain. Anyway, I'll talk to him about getting you better accommodations"

Misty was fuming now. "You arrogant prick let me out right now!"

"No can do twerp" Shadow laughed.

Misty reached out and yanked shadow by the neck slamming him into the cell. The loud clang reverberated through the air.

"Let me out right NOW!" she had Shadow in headlock his head pressed into the bars of the door. Shadow tried to pull away but Misty tore off the cloth covering his face in the process. As Shadow fled, she could only see the back of his head covered in lavender hair.


	4. Motives

Ash Ketchum walked down the grey hallway of the Son's of Pallet Town Head Quarters. He had grown much over the course of the war with Team Rocket. He had become a well-muscled man. Not as buff as say Kain and nowhere near the size Bruno was before he died. His hair still looked like he had never put a comb to it in his life. He wore an old pair of blue jeans and a dusty leather jacket.

"How was the meeting?" the voice of his long time friend and rival Gary Oak startled him. Ash turned to his friend who also never combed his hair.

Ash sighed holding his hands to the back of his head.

"It stunk the women are still offended that its called the Son's of Pallet town and not the Children of Pallet town or some other PC crap." Gary just laughed.

"Yeah they just don't understand we founded this group so we get to name it"

The two stood in silence for what felt like an eternity.

"Any word from Misty?" Gary asked.

Ash's face fell at the mention of that name.

"No we sent a message to the Vapor Vengeance days ago we haven't gotten a response"

At that moment, the familiar voice of Brock came over a loud speaker.

"Commander Ash, Commander Gary please comes to Base Command"

The two turned around and started sprinting down the corridor.

They soon entered the room titled base command. It has the look of command center computers lining the walls. A giant sized map of Kanto sitting at the head of a large rectangular table. Various strategic points highlighted the map.

Two people sat at the table. The first was Brock the other was woman with long pink hair.

"Brock why did you shave your head?" Ash groaned.

Brock just smiled and said, "I thought it look cool"

"Its because we was going bald anyways he wanted everyone to think its by choice" the woman said coyly.

Brock decided to ignore that comment despite the muffled laughs he could hear.

"Ash I've got some Intel on the Vapor Vengeance sit down please"

Ash held his breath and sat down in the chair at the far end. Gary sat next to the pink haired girl.

Brock had a solemn look on his face.

"Ash the Vapor Vengeance has been captured by a Squad of Team Rocket agents several members of the rebel faction are dead."

Ash slammed his fist into the table, tears forming in her eyes. The pink haired woman collapsed into Gary's arms in tears.

"From what we know three days ago a squad of rockets found the Vapor Vengeance's hide out they captured or killed everyone inside. However"

The last word made everyone look up.

"The Squad was planning to stay behind to capture the leader namely Misty, when she returned to her hideout. The squad never reported in. The next morning the agents had been found dead and with no sign of Misty"

Ash looked up with a new look of hope in his eyes. "So Misty escaped but who killed those rockets"

The pink haired woman stopped drying her tears and looked to Brock. "So my little sister could still be alive." She hugged Gary tightly who kissed her lightly on the lips in response.

Brock gave a hopeful smile

"Evidence suggests Kain wiped out the rocket agents"

Ash stood up and started pacing.

"But do we know what happened to Misty?"

Brock could only shake his head in response.

"Kain might know where she is but he's not known for acts of charity if he saved her it was by accident or because he wants something form her"

"So what can we do?" the pink haired Lilly asked.

Brock shook his head. "I don't know Kain doesn't communicate with other rebels often most don't agree with his methods"

Gary raised an eyebrow and said. "You mean his reputation of butchering his enemies putting there head up on pikes."

Ash nodded "As far as I'm concerned he's no better then Giovanni, anyone who stands in his way gets hurt"

Lilly slid off Gary's lap and sat up in the chair to his right.

"Lets just hope Misty wasn't in his way"

Ash clenched his fists. "If he hurts her I swear I'll ripe out his black heart"

Gary gave a hearty laugh, "ha anyone who messes with Ashy boy's girlfriend had better beware!"

Ash's face blushed a deep red. "She's not my girl friend!"

Meanwhile back with Misty

Misty sat tied to a chair in a pitch-black room. The only source of light was a single bright bulb above her.

The shadowy figure of Kain stood somewhere in the dark.

The red head struggled against the ropes that bound her to the chair.

"Did you have to tie them so tightly you freak" she yelled fiery as ever.

Misty heard sinister laughter coming from the darkness of the room.

"Would you like me to untie you?" the voice of Kain spoke.

"Really would you do that?" Misty asked.

"Just ask" Kain said with a devilish smirk on his face.

Misty figured it couldn't hurt so.

"Could you untie me?" she asked sweetly pulling on the ropes.

"No" Kain said bluntly.

"Bastard, why am I here!" she hollered kicking her legs

"You have quite the temper but I'll be asking the questions" Kain said coldly.

Misty still couldn't see Kain anywhere; the only thing giving away is presence was his voice. He walked slightly over the cement floor.

Despite her fear, Misty kept her defiant face high.

Kain gave an indigent snort.

"I know your afraid Misty, I can sense these things, are you expecting your boyfriend to burst in the door and save you" Kain laughed as Misty's face turned beat red and she stuttered for words.

"Ash isn't my boyfriend he's a boy and my friend but not my boyfriend!"

Kain stepped out of the darkness and evil grin on his face.

"I never said anything about Ash"

At this point, it became impossible to tell if her red face was from embarrassment or her anger. It

Kain was quite amused and circled around Misty half his body under the single light the other half in shadow.

"Back to the matter at hand Misty, The main reason your are here is because I'm testing you"

Misty was baffled.

"Testing me for want?" she demanded using her best death glare.

Kain just smirked.

"You impress me Misty, those agents we're ready to kill you or worse had I not been following you they'd have had their way. Yet you stood proud despite your fear."

"Get to the point asshole" Misty yelled her flailing as best as she could against her bonds. In fact, she flailed so much the chair fell over. Luckily, her arms took the brunt of the impact instead of her head.

"Smooth" Kain mocked he knelt down and stood the chair up right. "This brings me to my second point I could kill you in the blink of the eye and yet you insist on insulting me." Kain said as he moved his face inches from Misty.

"Not even the great Sabrina could stand against me as fearless as you. Join me Misty join the Black Sword"

Misty was disgust. "I'd never join you, you're a monster!"

Kain just sighed. "I know"

"So what are you going to do with me keep me prisoner?"

Kain shook his head. "No I'll leave you somewhere for Ash to find.

Misty was shocked to say the least. "Just like that, I insult you spit in your face and you let me go?"

Kain smirked, "Sabrina and the High Guard know I have you I have do doubt they will inform Ash and the Son's of Pallet town. From what Shadow has told me about Ash. Your friend won't rest until your safe I don't want my secret base uncovered so its just easier to hand you over but not before I give him a little test".

Kain smirked and walked into the darkness. Then came the sound of a heavy metal door opening. Kain stopped in the doorway blotting out much of the light coming in from the door.

"Shadow take Misty back to her cell and make sure she gets something to eat before we leave to meet Ash"

"Yes Master Kain" Shadows voice said from right behind Misty.

Misty was startled and tried to turn her head towards the direction of Shadow's voice but couldn't get her head around far enough.

"How'd you get in here?" Misty questioned.

"I was here the entire time, Kain taught me the art of Ninjitsu" He said plainly.

"Guess you have the skills to match that cheesy Ninja outfit now untie me!" she screamed.

Shadow cut the ropes binding Misty's arms and swiftly moved in front of her. His face as covered by the ninja mask once again. Obviously recovered from after Misty tore it off.

"So James it is you" she said looking at Shadow.

"eh How'd you know it was me?" Shadow said removing his mask revealing it was indeed James.

Misty only shrugged. "How many people have lavender hair, so I guessed"

His face had changed much in the ten years sense she last saw him. It showed the changes of a decade of fighting and training. It had become rough and hard, a scar ran from his right eyebrow down to his cheek.

"Never could out smart you guys for long, Its nice to see you twerp" he gave a light smile.

Misty looked at him with wonder shaking her head in disbelief. What on earth could have happened to James in these past ten years.

"What happened to you where's Jessie, Is she still in Team Rocket?"

James was quite for a moment and a tear came to his eye.

"She's dead, she died because I couldn't protect her from Giovanni"

Misty gasped. "Oh James I'm so sorry"

James moved around her back and finished untying her. He spoke in a solemn voice filled with a lifetime of regret.

"I'd be dead now if not for Kain, I was ready to hang myself after Jessie died, but Kain found me and gave me a reason to live"

"Revenge." Misty finished as she stood up letting the ropes fall. She turned to James who had his back turned to her.

"I already knew how to lie and to cheat, Kain taught me how to fight, how to survive and how to kill." James clenched his fist and kicked the now empty chair away.

"The one thing he can't teach me is how to forget my pain or sorrow, but then he can't teach himself that either"

Misty held her fist over her heart a few tears started to run down her face. "You loved Jessie didn't you?"

James turned to her with a weak smile. "More then anything, I just wish I could have told her that before it was to late"

End of chapter:


	5. Reunion

Brocks voice broke Ash from his daze.

"Ash I think you should take this call" he said trying to shake if friend back to reality.

Ash just shook his head. "Let Gary handle it" he said solemnly.

"Its about Misty" he replied with a smirk. In a blink of an eye Ash was on his feet and had run down his friend in order to reach the phone. When he reached the videophone the screen was blank.

Brock was left twitching on the ground.

Gary was standing there holding the receiver. "Its Kain he says he has Misty" he whispered.

Ash picked up the phone.

"Be calm" Gary and Brock whispered.

Ash was as calm as he could possibly be, meaning he was screaming his head off.

"What have you done with Misty you bastard, give her back!"

Gary and Brock just hung their heads.

"Really clam Ash," they muttered.

Kain on the other end was currently holding the phone 2 feet from his ear waiting for the hearing in his right ear to return.

"If you're done screaming boy I'll tell you how you can get the girl back" Kain sneered.

Ash gulped and started to sweat.

"Just tell me what you want, just don't hurt her please I…"

Kain smirked. "Excellent, come to these coordinates north of pewter city and come alone" with that Kain hung up.

"Ash this smells like a trap!" Gary worried.

Ash gave a weak smile. "I know, but what choice do I have?" he asked before he left the room. As he walked out the door Brock muttered.

"Anything for the one you love."

While Ash was rushing off to his meeting with Kain, James or Shadow as he now called himself was stalking a few rockets in the forest.

Shadow hid around a tree watching the two agents load boxes onto a truck. He had been following them around the forest for hours trying to see what they were picking up but he still hand no clue

Shadow checked the three pokeballs he brought with him Houndoom, Cacturne the evolved form of his Cacnea and lastly Seviper. Shadow shed a few tears for his fallen lover.

James gripped the three pokeballs and threw them all at once.

The two rockets quickly responded releasing their pokemon.

"We're under attack," one of them yelled.

Scizor, Espeon and Mahamp.

"Houndoom use Smog attack, Seviper use Screech, Cacturne faint attack Espeon"

The three pokemon nodded and commenced the attack. The smog and screech filled the air and the faint attack sent Espeon into the ground.

It was then the rockets turn to attack.

"Espeon use psybeam on Seviper" the first rocket ordered. However, before Espeon could nail Seviper with psybeam, Houndoom used faint and blocked the attack.

"Dam you!" the second rocket yelled. Seviper then used poison fang on Machamp, which then mega punched the snake pokemon sending bouncing across the ground.

Scizor then used Metal claw launching a devastating attack on Cacturne sending him flying into a tree.

"Your going to lose rebel scum!" screamed the first agent.

Espeon tackled Cacturne who responded by using, Leech Seed, which started siphoning Espeons energy. Houndoom launched a fire blast at Scizor. The attack missed, striking the truck. A moment later, it exploded knocking out Espeon and Machamp. It also sent the two agents flying.

The Scizor looked around and sweat dropped before fleeing the scene.

Shadow smiled. "That was to easy," he laughed. He turned around and his expression changed to horror. Two-dreaded pokemon stood before him. The large arm blades ready for combat. With armored grey skin, muscles and a head that looked similar to that of an Alakazam.

"Oh shit!"

After several hours, Ash arrived at the meeting point. Kain was already there standing in the clearing his black cape blowing lightly in the wind.

"So you have arrived" a smug look was on Kain's face. "I'm surprised I thought you'd have gotten here sooner"

"I swear Kain if you've hurt Misty in any way I'll tear you're your heart with my bear hands!

Kain smiled, "Ash you surprise me, such a brutal threat the kind I'd make"

Ash shook his fist and glared menacingly. Ash was getting angrier by the minute he wanted Misty back now.

"What is it you want Kain?"

Kain took a deep breath and with a reflective look on his face said in is usual arrogant tone of voice said.

"I want revenge Ash, I had been trailing Misty for a few days to gain information. I saved her and made her a guest in my home"

"I offered her a job she turned me down, I had every intention of handing her over to you, Shadow told me you're like her boyfriend r"

Ash blushed with embarrassment.

"Now here's Misty" Kain stepped aside revealing a tied and gagged Misty who had been hidden behind him. Kain cut the ropes and removed the gag.

Once free Misty ran to Ash and hugged him tightly. Ash returned the hug and the two laughed happily.

"I'm so glad your alive, did he hurt you"

Misty smiled and rested her head on his shoulder.

"No he didn't scared the life out of me but never hurt me"

"Kiss her stupid" a small annoying voice said.

Ash and Misty, looked to Kain's feet and saw a Meowth sitting there.

"Kiss her stupid!" the cat pokemon said.

Ash's eyes went wide. "Is that…"

"Meowth what are you doing here?" Kain asked.

"Shadow's in trouble he needs your help"

"Where is he?" Kain demanded.

Ash was bewildered about the look of concern on Kain's face.

Kain looked to the still hugging couple. Ash's arms now around Misty's waist holding her close to him.

"Now if you excuse me I have a friend to rescue"

Ash narrowed his eyes. "I didn't think someone like you was capable of having a friend.

Kain smirked. "You may be right Ash but Shadow shares my goals and he's like a son to me" with that he was gone.

"Come on Misty I'll take you to my home"


	6. Treason and Truth

Part 5: The Council of Rocket.

In Viridian City, deep within Team Rocket head quarters, a secret meeting Giovanni's five commanders was unfolding. Giovanni was strangely absent from this meeting as well as one of the sixth commander. The room was dark and the faces obscured with the lack of light.

Three of these people you may already know.

Domino the Black Tulip and Vicious the Iron Masked Marauder, as well as for former Drill Sergeant Viper. The other two who happened to be there well you'll learn more about them later.

"We are gathered here today to disscuss how deal with the growing rebel problem" Domino stated plainly as she played with a black tulip in her hands.

"There is no rebel problem, they will be dealt with in time, after all we just took care of the Vapor's only a few days ago" answered Viper.

"They were a two bit rebel group, and there leader Misty managed to escaped. It means nothing" Said an elderly gray haired rocket named Oni.

"Only because Kain happened to intervene." Vicious said venomously.

"Kain is one of the key issues I wished to discuss today, which is why I called this meeting while Giovanni was busy on Project J" Domino's stare was piercing like a hot knife through butter.

After a brief pause she continued.

"I purpose attempting to make an peace with Kain, perhaps even an alliance."

The room was filled with quite laughter, until red head with a deep southern accent slammed her fist into the table silencing the others.

"You know fully well Kain hates and despises us. What makes you think he'll give up on his revenge?" she yelled.

Domino just smiled. "Oh its quite simple, what Kain wants above everything is Giovanni. Had Giovanni not betrayed him ten years ago or at least managed to kill him? I purpose we offer Giovanni to Kain in exchange for him to cease all activities against us."

"That's treason, Domino you could be executed on the spot for just discussing it!" yelled the southern bell.

"Why should we continue to follow Giovanni while he hordes all the power" remarked Oni.

"Your plan has merit, Kain not only possess supernatural abilities but as a former elite agent he may still have access to our computer net work." Vicious added.

"But weren't his access codes purged after he left Team Rocket over 20 years ago." Viper remarked.

"Perhaps" Domino added, "however, Kain has shown a remarkable ability to gather intelligence on our movements behind any of the other rebel groups."

Oni pondered for a moment. "Do you think Kain was given some special access by Madam Boss so Giovanni couldn't remove him completely?"

"That's exactly what I think, remember Kain was in team rocket before any of us when Giovanni was just a child" Domino answered.

"I suppose we should put it to a vote" Viper answered.

"What about the sixth Domino he isn't here?" Oni stated.

"Don't worry about him I already have his support" she answered simply.

"All in favor raise your hand" Vicious said.

Domino, Viper, Oni, and Vicious, all raised their hands.

"All opposed?" asked Domino despite the obvious answer.

The southern bell raised her hand.

"You people are mad Giovanni will kill you all for your treachery" she yelled.

The others just laughed sinisterly.

"My dear the only threat to our plan is you" Vicious said.

Domino stood up leaving her tulip on the table. She walked over to the southern bell. "Say goodbye to everyone" the Black Tulip smiled as she led her away. Once outside the meeting room Oni noticed the suit case left on the table.

Walking over he opened it up and saw it was full of her trade mark black tulips.

"Hey Domino your forgot your suit case full of your explod…. Oh shit" the last words died in this thought as the explosion filled the room.

The southern bell looked quite surprised and relieved.

"So it was all a setup?" she asked.

Domino smiled.

"Of course three traitors dead, Giovanni will be pleased with our loyalty"

Sometime later…

Ash burst into the door of the command room of the Son's of Pallet Town with Misty at his side.

Needless to say Misty was quite happy to see her sister Lily again and quite shocked to see a bald Brock and her sister in Gary's lap.

"MISTY!" Lilly squealed.

"LILLY!" Misty answered back the two sisters embraced and cried tears of joy to see each other once again.

Ash and Brock smiled at Misty's reunion. Gary just laughed and walked up to his wife Lilly.

Lilly and Misty's reunion embrace soon ended.

"Misty, I know you've already meet but I'll introduce you anyway this is my husband Gary"

Misty's eyes widen with shock.

"Your married to HIM!" she shouted pointing her finger right in Gary's face.

"Hey, I take offence to that!"

Lilly laughed. "A lot has changed over the years I'm so glad your ok"

Misty smiled. "Its good to see you too, I was so worried."

"We were all really worried about you, did Kain hurt you or anything?" she held Misty's hands greatly concerned over her sisters well being.

"I'm fine, we was surprisingly polite, for an arrogant SOB" Misty answered.

This time Brock went up and gave Misty a friendly hug.

"Out of all of us though Ash more worried then the rest of us but together."

Lily shrugged and said. "Of course what kinda boyfriend wouldn't fret over his girl"

"ITS NOT LIKE THAT!" Both Ash and Misty screamed in unison blushing as red as a tomato. Once they realized they said the something they blushed even more while the others just laughed at their embarrassment.

Ash moved up closer to Misty's side.

"So what did he want with you?"

Misty pondered this for a moment,

"I don't really know he offered me a position in his organization I turned him down of course, but the strange thing in he wasn't at all surprised. It was as if the offer was some kind of cover"

Brock rubbed his chin attempting to look more dignified. It didn't stop Misty from staring at his head.

"So Brock lost all his hair?" she whispered to Ash.

"Pretty much"

Brock finally spoke.

"Hmm that is strange, we don't really know a lot about Kain, other then rumors mostly around his supposed supernatural powers"

Misty shook her head. "I don't know I watched him fight first hand, It's more then simple tricks and misdirection. I think I believe those stories."

Ash suddenly remembered the events that transpired when he got Misty back.

"Hey guys I just remembered. I think I saw meowth talking Kain, the meowth"

Brock looked so surprised you could almost see his eyes.

"Are you sure, Meowth?"

"Do you know of any other talking cat pokemon?" Ash answered.

"Why would Meowth be working with Kain against team rocket?" Gary questioned.

Misty sighed deeply, "I know why, while I was held prisoner, I learned that Kain's lieutenant Shadow is really James…" the last words trailed off as Misty held back the tears.

"So Jessie and James are working for Kain now?" Ash question.

At this point Misty couldn't hold back her tears any longer.

"James told me that… he said that Jessie she died. James is working for Kain because he wants revenge"

A solemn silence filled the air as the reality set in.

"You know those two were always up to no good but.." Ash's voice trailed.

"But they didn't deserve that, they weren't all bad, helped us save the world a few times" Brock finished.


	7. Origins

Chapter 6: Dark Origins.

Kain moved swiftly through the woods Shadow had gotten in over his head and he'd be damned if he let him die before they could have there revenge. As he ran to his last known location he remembered the day they met they day he claimed his power.

One decade earlier.

It was dawn of a new age, the elite four had fallen and Giovanni's army of cloned pokemon marched across Kanto. Soon he would have complete control over the continent

Kain limped through the woods obviously suffering from numerous injuries. Among them was obviously a broken arm. He had been walking all night, he knew if he went to sleep it was unlikely he would ever wake up again. Though he longed for death, he longed for revenge far more.

'_Just a little further, I should be able to reach vault by nightfall'_ Kain thought as he desperately tried to walk on despite the pain that racked his body.

It was then he heard voices, the first had a really heavy accent.

"James stop, what good is killing yourself going to do. It won't bring back the dead"

Kain stopped for a moment, and listened closer.

"I have nothing left, she'd dead because I couldn't protect her." Said a sobbing male voice.

'_He's like me'_ Kain thought.

The accented voice answered back.

"Hey I hate myself for not being able to save her from Giovanni too but what good is you dying going to do?"

Kain's eyes widen with shock.

'_Whoever he is we share the same pain" _Kain thought before changing course towards the voices.

Soon Kain reached the clearing and saw a lavender haired boy preparing to hang himself from a tree. A small meowth franticly trying to reach up to fury swipe the rope only to be knocked down when ever he leaped up.

It was then James noticed the visitor in the clearing.

"Who are you… and what happened to you?" James asked noticing Kain's obvious injured state. Meowth took this opportunity to slice with his claws causing James to tumble to the ground.

Kain wrenched in pain before choking out an answer.

"I over heard you and your friend talking, As for what happened to me, Giovanni"

Kain spat Giovanni's name from his mouth. He then looked around and asked.

"Where is your friend by the way?"

Meowth stood up and answered proudly.

"I'm right here!"

As Kain stood dumb founded by the talking pokemon, James took this moment to speak.

"So Giovanni did that huh not surprising. He... •choke• killed my best friend, the woman… the woman I loved" James was quickly overcome with tears at Jessie's memory.

Kain understood James's pain knew it all to well.

"Giovanni killed my only child the only family I had left." Kain's answer struck James to his core.

"So what do we have to live for"

Kain smiled the first real smile he had in years.

"Revenge, revenge on Giovanni and all of Team Rocket for what they've done to us"

Meowth just shook his head solemnly.

"No offense but you look like you have one foot in the grave already"

"That I am, but north of here is an ancient power, a weapon of sorts that was locked way by the founding members of Team Rocket, with that we can have our revenge"

James looked this broken man and pondered his options, death or vengeance…

He chose vengeance.

Several hours later the trio was approaching their destination. Though only Kain really knew how close they were. James had been supporting much of Kain's bulk during this journey.

"_Why do I trust this man?, I don't know him he didn't even say his name. Can this power he spoke of really help me avenge Jessie's death." _These questions raced though James mind though the words never reached his lips.

"Hey I never caught your name" James finally spoke breaking the long silence.

Kain's response was as cold and quick. "The man I was is dead, what remained of him died with his family, call me Kain."

"I'm James"

"I know I overheard your Meowth earlier, you might want to think about a new name too"

"Well then you can call me shadow, because I'm a shadow of my former self"

"ha ha hack!" Kain's laugh ended with a bloody cough. It was when James took note that the moist feeling on his back wasn't sweet but the blood of the man he was helping up the mountain trail.

"_I don't think he's going to make it" _Meowth thought. "_But even if he doesn't maybe me and James can use dat weapon he was talking about if not at least this guy won't have to die all alone in wilderness."_

They soon pasted by an opening in the mountain, barley visible behind some trees and shrubs.

"Through there" Kain rasped his voice growing weaker.

James only nodded and helped him into the darkness.

Meowth produced a flashlight from James pack to light the way.

As they marched through the dank cave James noticed his load felt lighter. Kain felt it too he could feel his strength returning or his will his hunger for revenge over powered his broken body.

Finally the trio reached what appeared to be a dead end. Kain took his arm from James and staggered over to a large stalagmite.

Kain flipped the top revealing it to be a false rock. There was a load rumble was the wall of the cave appeared to fall away. With the camouflage fell revealing a large double metal door with the familiar emblem of a red R sunken into the face.

James and Meowth were shocked to say the least.

"This is one of Giovanni's weapons?" James asked.

Kain shook his head; "Giovanni? That brat was barley old enough to have a trainer's license when this vault was locked.

Kain walked slowly towards the door working on a memory he once tried desperately to forget.

He moved to small keyboard in the door and punched in several letters.

N•O•F•A•T•E

"Verifying Authorization… password accepted, please enter primary password." The computer voice said.

"Dam that old witch, figures only her password would do any good" Kain muttered to himself.

He then punched in the letters I•A•M•G•O•D.

Primary password accepted.

"Thank you madam ego" Kain rasped.

"Who was Madam Ego?" Meowth asked.

"We called her Madam Boss she's Giovanni's mother"

James and Meowth both looked at each other as the massive metal doors opened wide revealing the ancient ruins inside. An old generator in the corner rumbled to life various lamps scattered across the room lit up.

James and Meowth followed Kain as he walked into these ancient ruins by the looks of the scattered and long abandoned equipment there was once some kind of agrological dig here.

James was in awe; it was as if the mountain swallowed an ancient city. Numerous statues of dark pokemon in various states of decay littered the area.

He then caught site of Kain once again as the man approached a pedestal. Upon that stone

displayed like a holy icon a black stone roughly the size of baseball but a perfect sphere. Kain walked carefully up to the pedestal, avoiding the tangle of extension cords that sent power from the generator to the lamps.

He blew away the layer of dust covering the pedestal and plaque beneath it.

The plaque read.

_May the orb of darkness be sealed here for all time._

_Let not It's power be unleashed._

_For all you care for will suffer and die._

_Should the darkness be set free._

"What a fool I was" Kain muttered as the tears flowed down his cheeks.

"I feared your power, feared it would turn me into a monster to destroy all I loved" his voice trailed off as pain wracked his battered body.

"Now all that I loved is dead and dust, what is left for the monster to destroy but my enemies?"

Kain reached out and grasped the orb in his hands. As black lightning flashed through the air he felt the power surge into his body. The cuts and burses covering his body disappeared. Kain let out a scream of pain and fell to his knees. James and Meowth rushed over to help Kain up, but he refused and rose to his feet unaided.

Kain stood transformed his wounds gone he looked stronger and a thousand times more deadly then before.

"So it is true then, you can not escape your fate"

Back to the Present +2 or 3 hours.

Kain carried a wounded James over his shoulders, behind him lay the carnage of a difficult battle against Giovanni's troopers.

"You know Shadow, I thought we got past this whole suicide thing a decade ago?"

"You're an asshole Kain." James responded.

End of Chapter.


End file.
